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Advances in Genetics and Phylogenomics of Tree

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 December 2024 | Viewed by 6714

Special Issue Editor

Prof. Dr. Peng Zhao

E-Mail Website
Guest Editor
Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
Interests: genomics; gene expression; evolutionary botany; gene family; molecular markers; DNA methylation; phylogenomic; sub-genomes; genome-wide association studies (GWASs); genetic diversity; domestication
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genomes, chloroplast genomes, genetics, gene families, DNA methylation, and gene expression networks pose important and increasingly concerning scientific questions with regard to forest tree species. These topics overlap with forest sciences in several areas, including molecular plant science, tree genomes, genetic diversity, phylogenetic, evolutionary application, gene expression, population genetics, and molecular breeding. Nowadays, sequencing technologies are quickly being developed through the efforts of academic researchers, a general application for genomes, chloroplast genomes, and transcriptome sequencing data. Therefore, advances in genetics and genomes data for the study of forest tree species are urgently needed. This Special Issue will provide an overview of the latest advances in the field of genomes, chloroplast genomes, and phylogenomic trees and their applications in diverse areas. Selected contributions on advances in genetics, characterization, and molecular applications of these data in tree species will be presented.

Prof. Dr. Peng Zhao
Guest Editor

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Keywords

  • genomics
  • gene expression
  • gene family
  • DNA methylation
  • phylogenomic
  • genome-wide association studies (GWASs)

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Published Papers (6 papers)

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Research

19 pages, 5949 KiB  
Article
Genetic Diversity and Association Analysis of Traits Related to Water-Use Efficiency and Nitrogen-Use Efficiency of Populus deltoides Based on SSR Markers
by Chengcheng Gao, Cun Chen, Ning Liu, Fenfen Liu, Xiaohua Su, Chenggong Liu and Qinjun Huang
Int. J. Mol. Sci. 2024, 25(21), 11515; https://doi.org/10.3390/ijms252111515 - 26 Oct 2024
Viewed by 588
Abstract
Populus deltoides is one of the primary tree species for bioenergy production in temperate regions. In arid/semi-arid northern China, the scarcity of water and nitrogen significantly limits the productivity of poplar plantations. The identification of relevant molecular markers can promote the breeding of [...] Read more.
Populus deltoides is one of the primary tree species for bioenergy production in temperate regions. In arid/semi-arid northern China, the scarcity of water and nitrogen significantly limits the productivity of poplar plantations. The identification of relevant molecular markers can promote the breeding of resource-efficient varieties. In this study, 188 genotypes of P. deltoides from six provenances served as experimental material. Genetic differentiation analysis, analysis of molecular variance (AMOVA), principal coordinate analysis (PCoA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and genetic structure analysis were performed using selected simple sequence repeat (SSR) markers. Based on these analyses, the association analysis of water-use efficiency (WUE) and nitrogen-use efficiency (NUE) were conducted using general linear model (GLM) and mixed linear model (MLM) approaches. The results showed that 15 pairs of SSR primers successfully amplified across all 188 individuals, with an average of 7.33 alleles (Na) observed per primer pair. The polymorphism information content (PIC) ranged from 0.060 to 0.897, with an average of 0.544, indicating high genetic diversity in the selected markers. The average inbreeding coefficient intra-population (Fis), inbreeding coefficient inter-population (Fit), and inter-population genetic fraction coefficient (Fst) values were 0.005, 0.135, and 0.132, respectively, indicating high heterozygosity, substantial inbreeding within populations, and moderate genetic differentiation, with an average gene flow (Nm) of 1.964, suggesting substantial gene flow between populations. Additionally, molecular variance was primarily within individuals (84.12%). Genetic structure analysis revealed four subgroups, with some degree of genetic admixture among the provenances. In the GLM model, 11 markers were significantly associated with five traits (p < 0.05), with an average contribution rate of 15.82%. Notably, SSR132 and SSR143 were significantly associated with multiple traits (p < 0.05). The MLM model identified two markers (SSR47 and SSR85) significantly associated with ground diameter (p < 0.05) and one marker (SSR80) significantly associated with NUE (p < 0.05). This study identifies loci associated with WUE and NUE, laying a foundation for future genetic improvement and marker-assisted breeding strategies in poplar. Full article
(This article belongs to the Special Issue Advances in Genetics and Phylogenomics of Tree)
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12 pages, 1305 KiB  
Article
Intra-Phenotypic and -Genotypic Variations of Beauveria bassiana (Bals.) Vuill. Strains Infecting Aedes aegypti L. Adults
by Norma Zamora-Avilés, Alonso A. Orozco-Flores, Teodora Cavazos-Vallejo, César I. Romo-Sáenz, David A. Cuevas-García, Ricardo Gomez-Flores and Patricia Tamez-Guerra
Int. J. Mol. Sci. 2024, 25(16), 8807; https://doi.org/10.3390/ijms25168807 - 13 Aug 2024
Viewed by 830
Abstract
Beauveria bassiana has potential for Aedes aegypti biological control. However, its efficacy depends on the strain’s geographic location, host susceptibility, and virulence. The present study aimed to evaluate the effectiveness of B. bassiana strain BBPTG4 conidia in controlling Ae. aegypti adults and its [...] Read more.
Beauveria bassiana has potential for Aedes aegypti biological control. However, its efficacy depends on the strain’s geographic location, host susceptibility, and virulence. The present study aimed to evaluate the effectiveness of B. bassiana strain BBPTG4 conidia in controlling Ae. aegypti adults and its detection via introns profile on exposed mosquito corpses. Morphologic characteristics among strains were highly similar. Comprehensive testing of these strains demonstrated that BBPT4 exhibited the ideal biological activity for Ae. aegypti control, with a median lethal time (TL50) of 7.5 d compared to ~3 d and ~10 d for BB01 and BB37 strains, respectively. Infected mosquitoes died after GHA and BBPTG4 exposure, and corpses were analyzed for infecting strains detection. Differences among the seven evaluated strains were determined, assessing five different insertion group I intron profiles in BBTG4, BB01, GHA, BB37, and BB02 strains. Mosquitoes infected by BBPTG4 and non-exposed (negative control) intron profiles were obtained. We detected the presence of introns in the BBPTG4 strain, which were not present in non-exposed mosquitoes. In conclusion, B. bassiana strains showed similarities in terms of their cultural and microscopic morphological characteristics and biologicals virulence level, but different intron profiles. BBPTG4 strain-infected Ae. aegypti adult corpses, showing specific amplicons, enabled us to identify B. bassiana at the strain level among infected mosquitoes. However, monitoring and detection of field-infected insects is essential for further verification. Full article
(This article belongs to the Special Issue Advances in Genetics and Phylogenomics of Tree)
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20 pages, 5487 KiB  
Article
Genome-Wide Identification, Expression Analysis under Abiotic Stress and Co-Expression Analysis of MATE Gene Family in Torreya grandis
by Hang Shen, Ying Hou, Xiaorong Wang, Yaru Li, Jiasheng Wu and Heqiang Lou
Int. J. Mol. Sci. 2024, 25(7), 3859; https://doi.org/10.3390/ijms25073859 - 29 Mar 2024
Cited by 2 | Viewed by 1162
Abstract
The multidrug and toxin efflux (MATE) family participates in numerous biological processes and plays important roles in abiotic stress responses. However, information about the MATE family genes in Torreya grandis remains unclear. In this study, our genome-wide investigation identified ninety MATE genes in [...] Read more.
The multidrug and toxin efflux (MATE) family participates in numerous biological processes and plays important roles in abiotic stress responses. However, information about the MATE family genes in Torreya grandis remains unclear. In this study, our genome-wide investigation identified ninety MATE genes in Torreya grandis, which were divided into five evolutionary clades. TgMATE family members are located on eleven chromosomes, and a total of thirty TgMATEs exist in tandem duplication. The promoter analysis showed that most TgMATEs contain the cis-regulatory elements associated with stress and hormonal responses. In addition, we discovered that most TgMATE genes responded to abiotic stresses (aluminum, drought, high temperatures, and low temperatures). Weighted correlation network analysis showed that 147 candidate transcription factor genes regulated the expression of 14 TgMATE genes, and it was verified through a double-luciferase assay. Overall, our findings offer valuable information for the characterization of the TgMATE gene mechanism in responding to abiotic stress and exhibit promising prospects for the stress tolerance breeding of Torreya grandis. Full article
(This article belongs to the Special Issue Advances in Genetics and Phylogenomics of Tree)
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22 pages, 12582 KiB  
Article
Genome-Wide Identification and Expression Pattern Analysis of BAHD Acyltransferase Family in Taxus mairei
by Donghuan Xu, Zhong Wang, Weibing Zhuang, Fan Zhang, Yinfeng Xie and Tao Wang
Int. J. Mol. Sci. 2024, 25(7), 3777; https://doi.org/10.3390/ijms25073777 - 28 Mar 2024
Viewed by 1163
Abstract
BAHD acyltransferases are involved in catalyzing and regulating the secondary metabolism in plants. Despite this, the members of BAHD family and their functions have not been reported in the Taxus species. In this study, a total of 123 TwBAHD acyltransferases from Taxus wallichiana [...] Read more.
BAHD acyltransferases are involved in catalyzing and regulating the secondary metabolism in plants. Despite this, the members of BAHD family and their functions have not been reported in the Taxus species. In this study, a total of 123 TwBAHD acyltransferases from Taxus wallichiana var. mairei genome were identified and divided into six clades based on phylogenetic analysis, of which Clade VI contained a Taxus-specific branch of 52 members potentially involved in taxol biosynthesis. Most TwBAHDs from the same clade shared similar conserved motifs and gene structures. Besides the typical conserved motifs within the BAHD family, the YPLAGR motif was also conserved in multiple clades of T. mairei. Moreover, only one pair of tandem duplicate genes was found on chromosome 1, with a Ka/Ks ratio < 1, indicating that the function of duplicate genes did not differentiate significantly. RNA-seq analysis revealed different expression patterns of TwBAHDs in MeJA induction and tissue-specific expression experiments. Several TwBAHD genes in the Taxus-specific branch were highly expressed in different tissues of T. mairei, suggesting an important role in the taxol pathway. This study provides comprehensive information for the TwBAHD gene family and sets up a basis for its potential functions. Full article
(This article belongs to the Special Issue Advances in Genetics and Phylogenomics of Tree)
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14 pages, 3607 KiB  
Article
Identification and Expression Analysis of R2R3-MYB Transcription Factors Associated with Flavonoid Biosynthesis in Panax quinquefolius
by Guimei Song, Yan Yan, Chun Guo, Jiankang Chen, Yumeng Wang, Yingping Wang, Jiaxin Zhang, Chang Gao, Junmei Lian, Xiangmin Piao and Peng Di
Int. J. Mol. Sci. 2024, 25(7), 3709; https://doi.org/10.3390/ijms25073709 - 26 Mar 2024
Cited by 2 | Viewed by 904
Abstract
Panax quinquefolius L. is an important medicinal plant, and flavonoids are among its main secondary metabolites. The R2R3-MYB transcription factor plays an irreplaceable role in plant growth, development, and secondary metabolism. In our study, we identified 159 R2R3-MYBs and analyzed their physical and [...] Read more.
Panax quinquefolius L. is an important medicinal plant, and flavonoids are among its main secondary metabolites. The R2R3-MYB transcription factor plays an irreplaceable role in plant growth, development, and secondary metabolism. In our study, we identified 159 R2R3-MYBs and analyzed their physical and chemical properties in P. quinquefolius. The protein length of 159 PqMYBs varied from 107 to 1050 amino acids. The molecular weight ranged from 12.21 to 116.44 kDa. The isoelectric point was between 4.57 and 10.34. We constructed a phylogenetic tree of P. quinquefolius and Arabidopsis thaliana R2R3-MYB family members, and PqMYB members were divided into 33 subgroups. Transcriptome data analysis showed that the expression patterns of PqMYBs in root, leaf, and flower were significantly different. Following the MeJA treatment of seedlings, five candidate PqMYB genes demonstrated a response. A correlation analysis of PqMYBs and candidate flavonoid pathway genes showed that PqMYB2, PqMYB46, and PqMYB72 had correlation coefficients that were higher than 0.8 with PqCHS, PqANS4, and PqCCoAMT10, respectively. Furthermore, a transient expression assay confirmed that the three PqMYBs were localized in the nucleus. We speculated that these three PqMYBs were related to flavonoid biosynthesis in P. quinquefolius. These results provided a theoretical basis and a new perspective for further understanding the R2R3-MYB gene family and the biosynthesis mechanism of secondary metabolites in P. quinquefolius. Full article
(This article belongs to the Special Issue Advances in Genetics and Phylogenomics of Tree)
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18 pages, 13230 KiB  
Article
Transcriptomic and Phenotypic Analyses Reveal the Molecular Mechanism of Dwarfing in Tetraploid Robinia pseudoacacia L.
by Yue Wu, Qi Guo, Cui Long, Yousry A. El-Kassaby, Yuhan Sun and Yun Li
Int. J. Mol. Sci. 2024, 25(2), 1312; https://doi.org/10.3390/ijms25021312 - 21 Jan 2024
Cited by 3 | Viewed by 1442
Abstract
Polyploid breeding techniques aid in the cultivation of new forestry cultivars, thus expanding the suite of strategies for the improvement of arboreal traits and innovation within the field of forestry. Compared to diploid Robinia pseudoacacia L. (black locust) ‘D26-5①’ (2×), its dwarfed homologous [...] Read more.
Polyploid breeding techniques aid in the cultivation of new forestry cultivars, thus expanding the suite of strategies for the improvement of arboreal traits and innovation within the field of forestry. Compared to diploid Robinia pseudoacacia L. (black locust) ‘D26-5①’ (2×), its dwarfed homologous tetraploid ‘D26-5②’ (4×) variety has better application prospects in garden vegetation guardrails and urban landscape. However, the molecular mechanism of the generation and growth of this dwarf variety is still unclear. Here, plant growth and development as well as histological differences between the diploid and its autotetraploid were investigated. Levels of endogenous hormones at three different developmental stages (20, 40, and 70 days) of 2× and homologous 4× tissue culture plantlets were assessed, and it was found that the brassinosteroid (BR) contents of the former were significantly higher than the latter. Transcriptome sequencing data analysis of 2× and homologous 4× showed that differentially expressed genes (DEGs) were significantly enriched in plant hormone synthesis and signal transduction, sugar and starch metabolism, and the plant circadian rhythm pathway, which are closely related to plant growth and development. Therefore, these biological pathways may be important regulatory pathways leading to dwarfism and slow growth in tetraploids. Additionally, utilizing weighted gene coexpression network analysis (WGCNA), we identified three crucial differentially expressed genes (DEGs)—PRR5, CYP450, and SPA1—that potentially underlie the observed ploidy variation. This study provides a new reference for the molecular mechanism of dwarfism in dwarfed autotetraploid black locusts. Collectively, our results of metabolite analysis and comparative transcriptomics confirm that plant hormone signaling and the circadian rhythm pathway result in dwarfism in black locusts. Full article
(This article belongs to the Special Issue Advances in Genetics and Phylogenomics of Tree)
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